Contact Information

Assistant Professor
Computational Structural Biology Lab., College of Life Sciences, Ritsumeikan University, Japan
1-1-1, Noji-higashi, Kusatsu-shi, Shiga, 525-8577, Japan
ktkshr <at>

Publication List


  • *: Corresponding author(s). / †: Joint first authors.
    1. †Naoki Ogasawara​, *†Kota Kasahara​​, Ryosuke Iwai, Takuya Takahashi,
      Unfolding of α-helical 20-residue poly-glutamic acid analyzed by multiple runs of canonical molecular dynamics simulations,
      2018, PeerJ, 6:e4769, doi: 10.7717/peerj.4769, URL
    2. *Kota Kasahara, Shun Sakuraba, Ikuo Fukuda,
      Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation,
      2018, The Journal of Physical Chemistry B, 122(9):2495-2503, doi: 10.1021/acs.jpcb.7b10830, PubMed URL
    3. Tomonori Hayami Kota Kasahara Haruki Nakamura *Junichi Higo,
      Molecular Dynamics Coupled with a Virtual System for Effective Conformational Sampling,
      2018, Journal of Computational Chemistry, , doi: 10.1002/jcc.25196, PubMed URL
    4. *†Kota Kasahara, *†Masaaki Shiina, Junichi Higo, Kazuhiro Ogata, Haruki Nakamura,
      Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state.,
      2018, Nucleic Acids Research, 46(5):2243-2251, doi: 10.1093/nar/gkx1297, PubMed URL
    5. *Junichi Higo, Kota Kasahara, BHaruki Nakamura,
      Multi-dimensional virtual system introduced to enhance canonical sampling.,
      2017, The Journal of Chemical Physics, 147: 134102, doi: 10.1063/1.4986129, PubMed URL
    6. Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara,
      OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation.,
      2017, Information Engineering Express, 3(2): 11-23, , URL
    7. *Kasahara K, Shiina M, Fukuda I, Ogata K, Nakamura H,
      Molecular mechanisms of cooperative binding of transcription factors Runx1–CBFβ–Ets1 on the TCRα gene enhancer.,
      2017, PLoS ONE, 12(2): e0172654, doi:10.1371/journal.pone.0172654, URL
    8. *Junichi Higo, Kota Kasahara, Bhaskar Dasgupta, Haruki Nakamura,
      Enhancement of canonical sampling by virtual-state transitions,
      2017, The Journal of Chemical Physics, 146(044104):1-12, doi: 10.1063/1.4974087, PubMed URL
    9. Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara,
      An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL,
      2017, International Journal of Networked and Distributed Computing, 5(1):52-61, doi: 10.1109/ICIS.2016.7550743, URL
    10. Kota Kasahara, Ikuo Fukuda, Haruki Nakamura,
      IBiSA_tools: A Computational Toolkit for Ion-binding State Analysis in Molecular Dynamics Trajectories of Ion Channels ,
      2016, PLoS ONE, 11(12): e0167524, doi: 10.1371/journal.pone.0167524, PubMed URL
    11. Kota Kasahara, Benson Ma, Kota Goto, Bhaskar Dasgupta, Junichi Higo, Ikuo Fukuda, Tadaaki Mashimo, Yutaka Akiyama, Haruki Nakamura,
      myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme,
      2016, Biophysics and Physicobiology, 13:209-216, doi: 10.2142/biophysico.13.0_209, PubMed URL
    12. Kota Kasahara, *Kengo Kinoshita,
      Landscape of protein-small ligand binding modes.,
      2016, Protein Sci, 25(9):1659-71, doi: 10.1002/pro.2971, PubMed URL
    13. Kota Kasahara, Ikuo Fukuda, Haruki Nakamura,
      mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories,
      2016, Bioinformatics, 32(16):2531-3, doi: 10.1093/bioinformatics/btw129, PubMed URL
    14. Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita,
      Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction,
      2016, PLoS ONE, 11:e0150716, doi: 10.1371/journal.pone.0150716, PubMed URL
    15. *Junichi Higo, Bhaskar Dasgupta, Tadaaki Mashimo, Kota Kasahara, Yoshifumi Fukunishi, Haruki Nakamura,
      Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking.,
      2015, J Comput Chem, 36(20):1489-501, doi: 10.1002/jcc.23948, PubMed URL
    16. Kota Kasahara, Ikuo Fukuda, Haruki Nakamura,
      A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer-DNA Complex.,
      2014, PLoS ONE, 9:e112419, doi: 10.1371/journal.pone.0112419, PubMed URL
    17. Bhaskar Dasgupta, Kota Kasahara, Narutoshi Kamiya, Haruki Nakamura, *Akira R Kinjo,
      Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics,
      2014, PLoS ONE, 9:e91347, doi: 10.1371/journal.pone.0091347, PubMed URL
    18. Kota Kasahara, *Kengo Kinoshita,
      GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes.,
      2014, BMC Bioinformatics, 15:12, doi: 10.1186/1471-2105-15-12, PubMed URL
    19. Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita,
      Ion Concentration-Dependent Ion Conduction Mechanism of a Voltage-Sensitive Potassium Channel.,
      2013, PLoS ONE, 8:e56342, doi: 10.1371/journal.pone.0056342, PubMed URL
    20. Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita,
      Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions.,
      2013, J Chem Inf Model, 53:241–248, doi: 10.1021/ci300377f, PubMed URL
    21. *Takeshi Obayashi, Kozo Nishida, Kota Kasahara, Kengo Kinoshita,
      ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.,
      2011, Plant Cell Physiol, 52:213–219, doi: 10.1093/pcp/pcq203, PubMed URL
    22. *Kota Kasahara, Kengo KinoshitK, Toshihisa Takagi,
      Ligand-binding site prediction of proteins based on known fragment-fragment interactions.,
      2010, Bioinformatics, 26:1493–1499, doi: 10.1093/bioinformatics/btq232, PubMed URL
    23. Kota Kasahara, Hideyuki Tsuboi, Michihisa Koyama, Akira Endou, Momoji Kubo, Calros Adriel Del Carpio, *Akira Miyamoto,
      Tight-Binding Quantum Chemical Molecular Dynamics Study on First Proton Transfer Process of ORR Catalyzed by Cobalt-Porphyrin Complex.,
      2006, Electrochem Solid-State Lett, 9:A490, doi: 10.1149/1.2336985, URL

    Reviews (Japanese)

    1. Kasahara K, Shirota M, Kinoshita K Molecular dynamics simulation, ion channel, dynamic structure, bioinformatics 2013 Seikagaku 85(8):656-662 PubMed

    Books (Japanese)

    amazon amazon


    Curriculum Vitae


    Jan 8th, 1983
    Hello, world.
    Department of Material Engeneering, Nagaoka College, National Institute of Technology, Japan
    Department of Applied Chemistry, School of Engeneering, Tohoku University
    Undergraduate student
    (Supervisor: Prof. Akira Miyamoto)
    Department of Applied Chemistry, Graduate School of Engeneering, Tohoku University
    Master course student
    (Supervisor: Prof. Akira Miyamoto)
    Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo
    Ph.D. course student
    (Supervisor: Prof. Toshihisa Takagi)
    Research Fellow of the Japan Society for the Promotion of Science (DC2)
    Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University
    (PI: Prof. Kengo Kinoshita)
    Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University
    (PI: Prof. Haruki Nakamura)
    Department of Bioinformatics, College of Life Sciences, Ritsumeikan University
    Assistant Professor.
    (PI: Prof. Takuya Takahashi)

    Affiliated Academic Organizations

    • Protein Science Society of Japan
    • Biophisical Society of Japan
    • Japanese Society for Bioinformatics